How does consciousness emerge from inert matter? This may be the hardest part of the "hard problem" that is consciousness. We have developed pretty solid models for explaining how the various modules and circuits in the brain work together (often in parallel processes) to create awareness and a sense of self.
But how does the brain itself, a three pound lump of fatty acids, produce consciousness? We don't really know, but the research presented below offers the beginning of a possible explanation, but only if the various models are combined (integrated) to generate a coherent theory.
Biological Photonic Communication in Cells
The open access arXiv.org Quantitative Biology platform (a service of the Cornell University Library) recently posted an article on biological photonic communication and information encoding in (otherwise known as biophotons) in loach fish eggs. Before taking a brief look at this article, here is some background on biophotonics.
Wikipedia offers a fairly neutral definition of biophotons, free from the New Age hype about divine light or other such nonsense, and also not as dismissive as some biologists in seeing "ultraweak bioluminescence" as meaningless.
A biophoton (from the Greek βίος meaning "life" and φῶς meaning "light"), synonymous with ultraweak photon emission, low-level biological chemiluminescence, ultraweak bioluminescence, dark luminescence and other similar terms, is a photon of light emitted from a biological system and detected by biological probes as part of the general weak electromagnetic radiation of living biological cells. Biophotons and their study should not be confused with bioluminescence, a term generally reserved for higher intensity luciferin/luciferase systems.Much of what we know about biophotons is a result of the work of German biophysicist Fritz-Albert Popp. Here is some additional background on biophotonics, including Popp's contribution, from the same Wikipedia article:
Biophotonics is the study, research and applications of photons in their interactions within and on biological systems. Topics of research pertain more generally to basic questions of biophysics and related subjects - for example, the regulation of biological functions, cell growth and differentiation, connections to so-called delayed luminescence, and spectral emissions in supermolecular processes in living tissues, etc.
The typical detected magnitude of "biophotons" in the visible and ultraviolet spectrum ranges from a few up to several hundred photons per second per square centimeter of surface area, much weaker than in the openly visible and well-researched phenomenon of normal bioluminescence, but stronger than in the thermal, or black body radiation that so-called perfect black bodies demonstrate. The detection of these photons has been made possible (and easier) by the development of more sensitive photomultiplier tubes and associated electronic equipment.
Biophotons were employed by the Stalin regime to diagnose cancer, and their discoverer, Alexander Gurwitsch was awarded the Stalin Prize. Various studies have indicated some potential for photon emission to be used as a diagnostic technique.  
In the 1970s the then assistant professor Fritz-Albert Popp, and his research group, at the University of Marburg (Germany) showed that the spectral distribution of the emission fell over a wide range of wavelengths, from 200 to 800 nm. Popp proposed that the radiation might be both semi-periodic and coherent.In the new article, Photonic Communications and Information Encoding in Biological Systems, by
Russian, German, and other biophotonics experts, often adopting the term "biophotons" from Popp, have theorized, like Gurwitsch, that they may be involved in various cell functions, such as mitosis, or even that they may be produced and detected by the DNA in the cell nucleus. In 1974 Dr. V.P.Kaznacheyev announced that his research team in Novosibirsk had detected intercellular communication by means of these rays. Until 1980s, Kaznacheyev and his team carried out about 12 000 experiments. Details of experiments are described in his book (in Russian).
Proponents additionally claim that studies have shown that injured cells will emit a higher biophoton rate than normal cells and that organisms with illnesses will likewise emit a brighter light, which has been interpreted as implying a sort of distress signal. These ideas tend to support Gurwitsch's original idea that biophotons may be important for the development of larger structures such as organs and organisms.
However injured cells are under higher levels of oxidative stress, which ultimately is the source of the light, and whether this constitutes a "distress signal" or simply a background chemical process is yet to be demonstrated. The difficulty of teasing out the effects of any supposed biophotons amid the other numerous chemical interactions between cells makes it difficult to devise a testable hypothesis. Most organisms are bathed in relatively high-intensity light that ought to swamp any signaling effect, although biophoton signaling might manifest through temporal patterns of distinct wavelengths or could mainly be used in deep tissues hidden from daylight (such as the human brain, which contains photoreceptor proteins). Recent review article  discusses various published theories on this kind of signaling and identifies around 30 experimental scientific articles in English in past 30 years which prove electromagnetic cellular interactions.
Sergey Mayburov (2012, May), the observed emission of photons generated by cells in fish eggs reveals a pattern that offers support for the theory that some cells use biophotons to communicate. While there is not, as of now, any definitive proof that cells (and some suspect DNA cells in particular) communicate through biophotonic emission, the evidence is accumulating.
Here is the abstract (and on a personal note, these authors need better translations - so many of these are clunky):
The structure of optical radiation emitted by the samples of loach fish eggs is studied. It was found earlier that such radiation perform the communications between distant samples, which result in the synchronization of their development. The photon radiation in form of short quasi-periodic bursts was observed for fish and frog eggs, hence the communication mechanism can be similar to the exchange of binary encoded data in the computer nets via the noisy channels. The data analysis of fish egg radiation demonstrates that in this case the information encoding is similar to the digit to time analogue algorithm.In a 2009 paper by the same author, Coherent and Noncoherent Photonic Communications in Biological Systems (based on a talk given at the 2009 Progress In Electromagnetics Research Symposium in Moscow), again examines biophoton emissions in frog and fish eggs. He concludes with the following:
If cells in eggs communicate via photons as a way to synchronize developmental stages (which is what the research has been attempting to demonstrate), then it seems logical to look for similar evidence in other complex systems of the body - and what system is more complex than the brain?In this paper it was shown that the exciton exchange supposedly constitutes the effective system of signalling and regulation of the bio-system development. It seems that such signalling to the large extent regulates the homogeneity of bio-system growth, preventing from the large fluctuations of its global form, i.e. defines its morphogenesis. In our approach, each cell cluster is the analogue of computer, which reaction is defined by the signals dispatched by the absorbed excitons(13). Basing on it, the simple scheme of information exchange inside the bio-system was proposed, from that the similar scheme of photons communications between the distant bio-systems was derived. It turns out to be analogous to the standard procedure of information exchange between the distant computers by means of photonic signals transferred by the optical fibres. It’s important to notice that the obtained scheme of photon communications is practically independent of particular BP [biophoton production] mechanism. The calculations of BP time spectra in our model are in a reasonable agreement with the experimental results for BP in fish eggs(1). Exploiting the rules of quantum optics, this model explains qualitatively the influence of external nonbiological irradiation on BP rate and ME [mitogenetic effect]. Note that this model doesn’t demand that e-m field of bio-systems will be coherent during the long time periods, it permit to obtain ME and other biophoton effects assuming the produced e-m field to be noncoherent.Yet it's worth to consider also the possibility that this e-m field of bio-system can possess the spacious short-time coherence within the observed photon bursts, similarly to the field coherence within the laser pulse. At least one experiment evidences directly that such coherence really takes place(11).
Biophotons, Microtubules, and Consciousness
Of special interest to me is the research into biophotonic activity in neurons (especially microtubules) and what role it may play in the emergence of consciousness - this is a topic on which there already has been considerable speculation. In 2004, Grassa, Klimab, and Kasper (Medical Hypotheses; 62, 169–172) published an article entitled, Biophotons, microtubules and CNS, is our brain a“Holographic computer”? Here is the abstract:
Several experiments show that there is a cell to cell communication by light in different cell types. This article describes theoretical mechanisms and subcellular structures that could be involved in this phenomenon. Special consideration is given to the nervous system, since it would have excellent conditions for such mechanisms. Neurons are large colourless cells with wide arborisations, have an active metabolism generating photons, contain little pigment, and have a prominent cytoskeleton consisting of hollow microtubules. As brain and spinal cord are protected from environmental light by bone and connective tissue, the signal to noise ratio should be high for photons as signal. Fluorescent and absorbing substances should interfere with such a communication system. Of all biogenic amines nature has chosen the ones with the strongest fluorescence as neurotransmitters for mood reactions: serotonin, dopamine and norepinephrine. If these mechanisms are of relevance our brain would have to be looked upon as a “holographic computer”.Several years later (2010), Rahnama, et al (J Integrative Neuroscience, 10:1, 65-88), published Emission of Biophotons and Neural Activity of the Brain, for which this is the abstract:
In this paper we argue that, in addition to electrical and chemical signals propagating in the neurons of the brain, signal propagation takes place in the form of biophoton production. This statement is supported by recent experimental confirmation of photon guiding properties of a single neuron. We have investigated the interaction of mitochondrial biophotons with microtubules from a quantum mechanical point of view. Our theoretical analysis indicates that the interaction of biophotons and microtubules causes transitions/fluctuations of microtubules between coherent and incoherent states. A significant relationship between the fluctuation function of microtubules and alpha-EEG diagrams is elaborated on in this paper. We argue that the role of biophotons in the brain merits special attention.The range of discussion on this topic is wide - from New Age woo to hard-core quantum computing models. On the side of woo, for those who might be interested or amused, this 2005 article by A.U. De and Dhananjay Pal, published in NeuroQuantology, entitled Significance of thought-carrying particles and thought-retaining particles in quantum measurement as well as cognitive problem, begins with this abstract:
The thought force a manifestation of universal consciousness, has been shown to be carried by thought-carrying particle in the inherent presence of thought retaining particle in a previous communication (Pal et al., 2004). The thought force (TF) is the origin of all the existing fields. While TCP is the origin of all the field particles (bosons), TRP is the origin of all the matter particles (fermions). TCP cannot exist without TRP and vice versa. Both TCP and TRP are interchangeable at supersymmetry having the same energy level. In ‘supersymmetry’, these TCP and TRP are inter-convertible to carry and retain a specific "thought" and also for its communication from one person to another. The human nervous system is evolved to provide an appropriate material structure to individualize consciousness, a characteristic of reality, pervading all manifestations. TCP and TRP are assumed here to be the ultimate constituents of matter as well as mind, an infinitesimal part of the universal mind (UM). These conceptual TCP/TRP can address many present day scientific enigmas some of which are detailed below."The thought force is the origin of all the existing fields." Okay, sure, you betcha. So that would mean that the universe, which we have determined to be 15 billion years old through a process of quantum measurement, is simply the result of human thoughts (one assumes it must be human) in various forms, even though modern humans have only been here for about 50,000 years. Or maybe it is the universal mind having these thoughts? Whatever. For these folks, biophotons act as TCP and/or TRP.
The researchers looking more specifically at neuronal structures and biophoton emission (BPE) offer much more legitimate explanations for how BPE might contribute to or delineate consciousness.
Returning to Grassa, Klimab, and Kasper (Medical Hypotheses; 62, 169–172) - Biophotons, microtubules and CNS, is our brain a“Holographic computer”? - they suggest that neurons are are perfect environments for biophotonic communication.
Neurons are large colourless cells with wide arborisations, they have a highly active metabolism generating photons, contain little pigment and have a prominent cytoskeleton consisting of hollow microtubules. As brain and spinal cord are protected from environmental light by bone and connective tissue, signal to noise ratio should be high for photons as signal.Interestingly, "hallucinogens have strong fluorescence properties, e.g., LSD, psilocybin, and harmine," which may offer some additional explanation for why LSD effects last 8-12 hours while the chemical cannot be detected in the body 30 minutes after ingestion. Anyway . . . .
Absorbing and fluorescent substances should interfere with such a biophoton communication system. Of all natural aminoacids, nature has chosen the aromatic ones with the strongest fluorescence, tryptophan, phenylalanine and thyrosine as precursors for the neurotransmitters involved in mood reactions: serotonin, dopamine and norepinephrine.
Also many hallucinogens have strong fluorescence properties, e.g., LSD, psylocibine and harmine. The capability of neuronal cells to generate a membrane potential enables them to release a lot of energy in short time by depolarisation. If depolarisation energy can be used to generate light, e.g., within the microtubules, the process of depolarisation could scan the information within the microtubules and MAP-proteins and transmit it to the next neuron. When depolarisation reaches the synapses the fluorescent neurotransmitters are released, the transmission is terminated and retrograde transmission inhibited.
The presence of light sensitive molecules in the brain suggests it's likely that they might be influenced by biophotons. Because biophotons likely would be absorbed by liquids, membranes, and other materials in the cell, Rhanama, et al (Journal of Integrative Neuroscience, 2010), hypothesize that microtubules act as wave guides, channeling light from one part of a cell to another.
Via Wikipedia, here is a brief overview of what microtubules are and the functions they perform.
Microtubules are a component of the cytoskeleton [in cells]. These rope-like polymers of tubulin can grow as long as 25 micrometers and are highly dynamic. The outer diameter of microtubule is about 25 nm. Microtubules are important for maintaining cell structure, providing platforms for intracellular transport, forming the spindle during mitosis, as well as other cellular processes. There are many proteins that bind to the microtubule, including motor proteins such as kinesin and dynein, severing proteins like katanin, and other proteins important for regulating microtubule dynamics.
Microtubules are the internal scaffolding of cells - they give structural support, but they also create pathways along which the cell's molecular machines move "freight" around the cell.
Rhanama and crew suggest that biophotons channeled by microtubules assist in coordinating activities in different parts of the brain. We already know that electrical activity in the brain is synchronized over inexplicable distances (at least at this point in time), but the electrical signals are too slow to coordinate brain activity, so it's probable that some other mechanism is active.
The teams of Grassa and Rhanama are not the first to point out that microtubules might play an important role in brain function and consciousness - but their inclusion of biophotonics elevates their model (in my opinion) above some competing models, such as the Orch OR model.
Orch OR - Microtubules, But No Biophotons
Stuart Hameroff and Roger Penrose published their Orchestrated Objective Reduction of Quantum Coherence in Brain Microtubules: The "Orch OR" Model for Consciousness in 1996, arguing that
consciousness is a function of quantum mechanics and that microtubules are the location in the brain where the (self-)collapse of the quantum wave occurs.
Here is the majority of the abstract for that paper:
The particular characteristics of microtubules suitable for quantum effects include their crystal-like lattice structure, hollow inner core, organization of cell function and capacity for information processing. We envisage that conformational states of microtubule subunits (tubulins) are coupled to internal quantum events, and cooperatively interact (compute) with other tubulins. We further assume that macroscopic coherent superposition of quantum-coupled tubulin conformational states occurs throughout significant brain volumes and provides the global binding essential to consciousness. We equate the emergence of the microtubule quantum coherence with pre-conscious processing which grows (for up to 500 milliseconds) until the mass-energy difference among the separated states of tubulins reaches a threshold related to quantum gravity. According to the arguments for OR put forth in Penrose (1994), superpositioned states each have their own space-time geometries. When the degree of coherent mass-energy difference leads to sufficient separation of space-time geometry, the system must choose and decay (reduce, collapse) to a single universe state. In this way, a transient superposition of slightly differing space-time geometries persists until an abrupt quantum classical reduction occurs. Unlike the random, "subjective reduction"(SR, or R) of standard quantum theory caused by observation or environmental entanglement, the OR we propose in microtubules is a self-collapse and it results in particular patterns of microtubule-tubulin conformational states that regulate neuronal activities including synaptic functions. Possibilities and probabilities for post-reduction tubulin states are influenced by factors including attachments of microtubule-associated proteins (MAPs) acting as "nodes"which tune and "orchestrate"the quantum oscillations. We thus term the self-tuning OR process in microtubules "orchestrated objective reduction"("Orch OR", and calculate an estimate for the number of tubulins (and neurons) whose coherence for relevant time periods (e.g. 500 milliseconds) will elicit Orch OR. In providing a connection among 1) pre-conscious to conscious transition, 2) fundamental space-time notions, 3) non-computability, and 4) binding of various (time scale and spatial) reductions into an instantaneous event ("conscious now", we believe Orch OR in brain microtubules is the most specific and plausible model for consciousness yet proposed.Hameroff has stayed with this model over the years, despite the lack of acceptance it has received among his fellow consciousness researchers. It would be interesting to see Hameroff work with some of the biophoton researchers, especially those who adhere to a microtubule model, to see if they might generate a more complete model.
One final group of researchers - Yan Sun, Chao Wang, and Jiapei Dai - offers a little more evidence for the neuronal communication mediated by biophotons in a paper entitled Biophotons as neural communication signals demonstrated by in situ biophoton autography (Photochemical & Photobiological Sciences, 2010; 9, 315–322).
Their study was essentially focused on developing new methods of detecting biophotons in neurons, but one of the outcomes was increased evidence that biophotons might serve as neural signals. This is from their discussion of the research results:
In the present study, we found that biophotonic signals generated by light stimulation consist of two components: action and background biophotons. A possible explanation for this observation is that external light stimulation might generate action biophotons, being able to conduct along the neural ﬁbers and result in an increase in biophotonic activity. Background biophotons are generated in situ, mostly by mitochondrial oxidative metabolism due to the lipid peroxidation of mitochondrial membranes initiated by the action of the respiratory electron transport system. In addition, the ﬁndings that almost no Ag granules could be observed in the spinal nerves after treating with both 1% procaine, and 50 mM 2-deoxy-D-glucose and 0.05% sodium azide, which can block neural conduction and oxidative metabolism, respectively, reinforce our explanation for the mechanism of IBA, as we discussed above, where the formation of visible Ag granules is due to a biophotonic effect, not because of other factors, such as chemical reactions.
Although we found that biophotons can be generated by external light stimulation and conducted along neural ﬁbers, implying that biophotons might serve as neural signals, there are a few questions that still need to be answered. For example, how do biophotons conduct along neural ﬁbers? What is the relationship between the biophotonic activity and bioelectronic activity in the nervous system? Although we have no direct experimental evidence to provide answers to these questions, a proposed mechanism called protein–protein biophotonic interactions may provide an explanation of the ﬁrst point based on previous studies showing that certain proteins, such as ﬂuorescent proteins, have unique characteristics of light absorption and emission.None of the evidence so far is conclusive, but some combination of biophotonics, microtubules, and quantum wave collapse might be the best possible explanation of the emergence of consciousness from matter.
Theories of consciousness tend to be more macro oriented, such as Global Workspace Theory, which explains how the various neural circuits (or modules) work together to generate a sense of self. However, we still need to explain how consciousness itself emerges from inert matter. One possibility is in the material presented above - but the future may bring newer and better models.